This paper gathers different investigations dedicated to pathological calcifications made of apatite in order to define the structural characteristics, which display a clinical significance. Such approach helps the clinician to define the characterisation tools, which have to be combined to obtain such structural characteristics in order to establish a possible relationship between the structural characteristics of the pathological calcifications and the disease. The fact that it is now possible to perform such experiments at the subcellular scale gives new opportunities for a large number of diseases associated to pathological calcification. Moreover, new diagnostic tools based on these characterisation techniques, quite sensitive to analyze microcrystals, can be defined.